### Regression test of NPT ensemble using flat files
### System: Water900
## Reading low temperature result
## Reading high temperature result
## Validating ensemble
Analytical slope of ln(P_2(H)/P_1(H)): 0.01309088
Trajectory 1 equilibration: First 0 frames (0.0% of trajectory) discarded for burn-in.
Trajectory 1 decorrelation: 135 frames (13.5% of equilibrated trajectory) discarded for decorrelation.
Trajectory 1 tails (cut = 0.10%): 2 frames (0.23% of equilibrated and decorrelated trajectory) were cut
After equilibration, decorrelation and tail pruning, 86.31% (864 frames) of original Trajectory 1 remain.
Trajectory 2 equilibration: First 2 frames (0.2% of trajectory) discarded for burn-in.
Trajectory 2 decorrelation: 0 frames (0.0% of equilibrated trajectory) discarded for decorrelation.
Trajectory 2 tails (cut = 0.10%): 2 frames (0.20% of equilibrated and decorrelated trajectory) were cut
After equilibration, decorrelation and tail pruning, 99.60% (997 frames) of original Trajectory 2 remain.
Overlap is 86.8% of trajectory 1 and 68.5% of trajectory 2.
A rule of thumb states that a good overlap is found when dT/T = (2*kB*T)/(sig),
where sig is the standard deviation of the energy distribution.
For the current trajectories, dT = 10.0, sig1 = 185.9 and sig2 = 195.3.
According to the rule of thumb, given T1, a good dT is dT = 8.0, and
                                given T2, a good dT is dT = 8.1.
Rule of thumb estimates that dT = 8.0 would be optimal (currently, dT = 10.0)
Computing log of partition functions using pymbar.BAR...
Using 469.00818 for log of partition functions as computed from BAR.
Uncertainty in quantity is 0.05581.
Assuming this is negligible compared to sampling error at individual points.
Computing linear fit parameters (for plotting / comparison)
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Linear Fit Analysis (analytical error)
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Free energy
    362.58564 +/- 21.60026
Estimated slope                  |  True slope
    0.010120  +/- 0.000603       |  0.013091 
    (4.93 quantiles from true slope)
Estimated dT                     |  True dT
    7.7    +/- 0.5               |  10.0  
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Computing the maximum likelihood parameters
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Maximum Likelihood Analysis (analytical error)
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Free energy
    372.18277 +/- 19.40976
Estimated slope                  |  True slope
    0.010390  +/- 0.000542       |  0.013091 
    (4.98 quantiles from true slope)
Estimated dT                     |  True dT
    7.9    +/- 0.4               |  10.0  
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Computing bootstrapped maximum likelihood parameters... [0/3]
Computing bootstrapped maximum likelihood parameters... [1/3]
Computing bootstrapped maximum likelihood parameters... [2/3]
Computing bootstrapped maximum likelihood parameters... [3/3]
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Maximum Likelihood Analysis (bootstrapped error)
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Free energy
    372.18277 +/- 12.09582
Estimated slope                  |  True slope
    0.010390  +/- 0.000338       |  0.013091 
    (7.99 quantiles from true slope)
Estimated dT                     |  True dT
    7.9    +/- 0.3               |  10.0  
==================================================
Calculated slope is 8.0 quantiles from the true slope
